To complement genetic studies being conducted on Drosophila melanogaster by investigators in NIDDK, we have applied field-emission scanning electron microscopy (SEM) to characterize a variety of Drosophila phenotypes with distinct thoracic associated malformations. These mutant phenotypes were compared to the wild type that served as a control. The flies were prepared for SEM using a sequential dehydration technique in increasing concentrations of ethanol, followed by step-wise chemical substitution with HMDS. The flies were mounted on stubs, sputter coated with 20 nm of gold, and digitally imaged in the SEM to reveal surface morphology. Of interest were landmarks on the thorax, such as the presence of clefts, cleft shape, number of clefts, and the presence or absence of hair. It was found that the SEM provided a considerably more detailed phenotype classification than could be achieved by optical imaging.